TABLE 1.
Major categories of H2O2-responsive elements in R. sphaeroidesa
| Category and RSP no. | Gene | Change atb:
|
Description | |
|---|---|---|---|---|
| 7 min | 30 min | |||
| H2O2 detoxification | ||||
| RSP0899 | ahpC | 2.2 | 1.8 | Alkyl hydroperoxide reductase |
| RSP0900 | ahpF | 1.8 | 1.2 | Alkyl hydroperoxide reductase |
| RSP2389 | 3.2 | 1.6 | Glutathione peroxidase | |
| RSP2395 | 0.22 | 1.0 | Cytochrome c peroxidase | |
| RSP2779 | katE | 69.2 | 4.5 | Catalase |
| Protein synthesis, maintenance, and repair | ||||
| RSP0166 | dksA | 0.05 | 0.63 | DnaK suppressor protein homolog |
| RSP0554 | 4.1 | 1.3 | HtpX protease | |
| RSP0559 | 3.6 | 1.5 | Peptide methionine sulfoxide reductase | |
| RSP1016 | 3.4 | 3.8 | Hsp20-type heat shock protein | |
| RSP1207 | 2.8 | 1.5 | Hsp33-type heat shock protein | |
| RSP1489 | 2.9 | 1.3 | Thioredoxin-domain-containing protein | |
| RSP1490 | 2.8 | 1.2 | ATP-dependent Lon-type protease | |
| RSP1529 | trxA | 1.9 | 2.4 | Thioredoxin |
| RSP1572 | 2.0 | 1.5 | Hsp20-type heat shock protein | |
| RSP1742 | 2.1 | 1.3 | Putative serine protease | |
| RSP2247 | 0.33 | 0.91 | Translation elongation factor EF-G | |
| RSP2248 | 0.56 | 0.56 | Translation elongation factor EF-G | |
| RSP2293 | clpA | 2.7 | 1.3 | ATPase with chaperone activity |
| RSP2310 | groES | 1.4 | 2.2 | GroES chaperonin |
| RSP3747 | 2.6 | 1.6 | Metallopeptidase | |
| RSP4127 | 7.9 | 1.1 | ATP-dependent Lon-type protease | |
| DNA damage repair/SOS response | ||||
| RSP0353 | dnaE2 | 6.5 | 2.8 | DNA polymerase III alpha subunit |
| RSP0452 | 2.8 | 3.2 | Homologous recombinase and LexA | |
| RSP0553 | ruvB | 2.0 | 1.7 | Holliday junction helicase |
| RSP0556 | ruvC | 1.9 | 2.0 | Holliday junction |
| RSP1997 | lexA | 3.7 | 4.0 | SOS-response repressor |
| RSP2354 | 4.0 | 1.4 | Vacuolar ATPase/ archaeal ATP synthase | |
| Iron transport and metabolism | ||||
| RSP0434 | sufD | 3.6 | 2.3 | FeS-cluster assembly/repair |
| RSP0435 | 5.4 | 2.8 | Possible frame-shift with sufD | |
| RSP0436 | 5.1 | 2.8 | Possible frame-shift with sufD | |
| RSP0437 | sufC | 8.3 | 3.4 | FeS-cluster assembly/repair |
| RSP0438 | 3.5 | 1.5 | Unknown | |
| RSP0439 | 8.1 | 2.5 | Conserved hypothetical protein | |
| RSP0440 | sufB | 9.6 | 2.6 | FeS-cluster assembly/repair |
| RSP0441 | sufB | 10.0 | 3.2 | FeS-cluster assembly/repair |
| RSP0442 | sufA | 9.4 | 1.2 | FeS-cluster assembly/repair, cysteine |
| RSP0443 | 11.2 | 1.6 | Conserved hypothetical protein | |
| RSP0862 | 1.9 | 0.83 | 3-Isopropylmalate dehydratase | |
| RSP0863 | 3.1 | 1.1 | large subunit | |
| RSP0904 | sitA | 4.0 | 1.1 | ABC-type Fe (III) transport system |
| RSP0905 | sitB | 2.4 | 0.91 | ATPase |
| RSP0906 | sitC | 1.8 | 1.0 | transporter |
| RSP0920 | exbB | 14.8 | 2.5 | Biopolymer transport protein |
| RSP0921 | exbD | 17.8 | 2.8 | Biopolymer transport protein |
| RSP0922 | tonB | 9.6 | 2.4 | Protein involved in iron transport |
| RSP1546 | bfr | 3.7 | 1.7 | Bacterioferritin |
| RSP1547 | bfd | 73.6 | 4.6 | Bacterioferritin-associated ferredoxin |
| RSP1806c | acnA | 5.4 | 0.91 | Aconitase |
| RSP1818 | feoB | 0.56 | 0.83 | Fe2+ uptake system protein |
| RSP1819 | feoA | 0.22 | 0.45 | Fe2+ uptake system protein |
| RSP2646 | edo | 6.0 | 1.3 | Phosphogluconate dehydratase |
| RSP2913 | 31.2 | 2.0 | Periplasmic iron binding protein | |
| RSP3074 | 2.2 | 0.91 | Dihydroxyacid dehydratase | |
| RSP3079 | 2.6 | 1.4 | Ferrichrome-binding periplasmic protein | |
| Metabolic changes | ||||
| RSP0446 | icdA | 4.7 | 1.1 | Isocitrate dehydrogenase |
| RSP0962 | 0.45 | 2.0 | 2-Oxoglutarate dehydrogenase | |
| RSP0964 | 0.42 | 1.8 | E2 component | |
| RSP0965 | 0.63 | 1.6 | E1 component | |
| RSP1078 | fdsC | 6.5 | 1.0 | NAD-dependent formate dehydrogenase |
| RSP1079 | fdsB | 8.4 | 1.2 | β subunit |
| RSP1256 | 0.31 | 1.3 | Enoyl-(acyl-carrier-protein) reductase | |
| RSP1257 | pbh | 0.24 | 1.2 | Poly-beta-hydroxyalkanoate (PHB) |
| RSP1806 | acnA | 5.4 | 0.91 | Aconitase |
| RSP1994 | gltA | 2.9 | 0.83 | Citrate synthase |
| Cell wall, lipo, and exopolysaccharide biosynthesis | ||||
| RSP0331 | bcsA | 0.40 | 0.91 | Cellulose synthase |
| RSP0332 | bcsB | 0.32 | 0.77 | Putative regulatory subunit |
| RSP0513 | 0.27 | 1.1 | Putative glycosyl hydrolase | |
| RSP0650 | 0.48 | 0.83 | Lytic murein transglycosylase | |
| RSP1461 | 2.1 | 1.0 | 3-Deoxy-d-manno-octulosonic-acid transferase | |
| RSP1462 | 1.9 | 1.0 | Tetraacyldisaccharide 4′-kinase UDP-3-O-3-hydroxymyristoyl N-acetylglucosamine deacetylase | |
| RSP2115 | 14.6 | 1.2 | UDP-3-O-3-hydroxymyristoyl N-acetylglucosamine deacetylase | |
| RSP2116 | 10.9 | 0.91 | Glucosamine-fructose-6-phosphate | |
| RSP2502 | 2.6 | 1.1 | UDP-N-acetylglucosamine uridyl transferase | |
| RSP2503 | 4.6 | 0.83 | ||
| RSP2550 | 2.4 | 1.3 | Endo-beta-1,3-1,4-glycanase | |
| RSP2716 | 0.48 | 0.91 | Lipid A disaccharide synthetase | |
| RSP3565 | 0.43 | 0.77 | Putative lysozyme | |
| RSP3838 | 0.48 | 0.83 | Cell surface polysaccharide export | |
| Highly regulated genes of unknown functiond | ||||
| RSP0557 | 9.0 | 2.3 | ||
| RSP0775 | 0.20 | 0.71 | ||
| RSP0820 | 0.23 | 0.71 | ||
| RSP0850 | 9.1 | 3.1 | ||
| RSP1170 | 5.2 | 0.45 | ||
| RSP1543 | 5.9 | 1.2 | ||
| RSP1544 | 6.2 | 1.0 | ||
| RSP1545 | 7.3 | 1.1 | ||
| RSP1548 | 73.0 | 4.9 | ||
| RSP1852 | 13.4 | 1.3 | ||
| RSP1948 | 6.0 | 1.9 | ||
| RSP2218 | 5.6 | 1.3 | ||
| RSP2234 | 5.1 | 1.8 | ||
| RSP2337 | 0.11 | 0.91 | ||
| RSP2624 | 34.1 | 28.5 | ||
| RSP2641 | 2.3 | 8.0 | ||
| RSP3078 | 8.5 | 1.7 | ||
| RSP3163 | 3.6 | 4.0 | ||
| RSP3361 | 0.19 | 0.56 | ||
| RSP3750 | 0.06 | 1.0 | ||
| RSP3751 | 0.05 | 1.2 | ||
| RSP3752 | 0.18 | 0.77 | ||
| RSP4160 | 0.11 | 0.50 | ||
| RSP4162 | 0.19 | 0.43 | ||
| RSP4164 | 0.24 | 0.77 | ||
a
Genes whose products are involved in energy generation, tetrapyrrole biosynthesis, and PS genes (shown in Fig. 1 and 2) are not included in this table.
b
Significant changes (according to criteria described in Materials and Methods) are in boldface. Selected genes that narrowly missed the cutoffs are included in this table to fully represent functional groups discussed.
c
Present in more than one category in this table.
d
Relative change (compared to no-stress conditions), >4 or <0.25.